<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
          "DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>BIP.Bayes.Melding</title>
  <link rel="stylesheet" href="epydoc.css" type="text/css" />
  <script type="text/javascript" src="epydoc.js"></script>
</head>

<body bgcolor="white" text="black" link="blue" vlink="#204080"
      alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="BIP-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/bayesian-inference">Project Homepage</a></th>
          </tr></table></th>
  </tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
  <tr valign="top">
    <td width="100%">
      <span class="breadcrumbs">
        <a href="BIP-module.html">Package&nbsp;BIP</a> ::
        <a href="BIP.Bayes-module.html">Package&nbsp;Bayes</a> ::
        Module&nbsp;Melding
      </span>
    </td>
    <td>
      <table cellpadding="0" cellspacing="0">
        <!-- hide/show private -->
        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="BIP.Bayes.Melding-pysrc.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<h1 class="epydoc">Source Code for <a href="BIP.Bayes.Melding-module.html">Module BIP.Bayes.Melding</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># -*- coding:utf-8 -*-</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"># Name:        Melding.py</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"># Purpose:     The Bayesian melding Class provides</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment">#              uncertainty analyses for simulation models.</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"># Author:      Fl&#225;vio Code&#231;o Coelho</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"># Created:     2003/08/10</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"># Copyright:   (c) 2003-2009 by the Author</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment"># Licence:     GPL v3</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">core</tt><tt class="py-op">.</tt><tt class="py-name">records</tt> <tt class="py-keyword">import</tt> <tt class="py-name">recarray</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">psyco</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt class="py-name">psyco</tt><tt class="py-op">.</tt><tt class="py-name">full</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">copy</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">cPickle</tt> <tt class="py-keyword">as</tt> <tt class="py-name">CP</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module BIP.Bayes.like=BIP.Bayes.like-module.html"><a title="BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-0', 'like', 'link-0');">like</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pylab</tt> <tt class="py-keyword">as</tt> <tt class="py-name">P</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">kde</tt> <tt class="py-keyword">import</tt> <tt class="py-name">gaussian_kde</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">linalg</tt> <tt class="py-keyword">import</tt> <tt class="py-name">LinAlgError</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">stats</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">,</tt> <tt class="py-name">zeros</tt><tt class="py-op">,</tt> <tt class="py-name">product</tt><tt class="py-op">,</tt> <tt class="py-name">exp</tt><tt class="py-op">,</tt> <tt class="py-name">ones</tt><tt class="py-op">,</tt><tt class="py-name">mean</tt><tt class="py-op">,</tt> <tt class="py-name">var</tt><tt class="py-op">,</tt><tt class="py-name">sqrt</tt><tt class="py-op">,</tt><tt class="py-name">floor</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">time</tt> <tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">random</tt> <tt class="py-keyword">import</tt> <tt class="py-name">normal</tt><tt class="py-op">,</tt> <tt class="py-name">randint</tt><tt class="py-op">,</tt>  <tt class="py-name">random</tt><tt class="py-op">,</tt> <tt class="py-name">seed</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module BIP.Bayes.PlotMeld=BIP.Bayes.PlotMeld-module.html"><a title="BIP.Bayes.PlotMeld" class="py-name" href="#" onclick="return doclink('link-1', 'PlotMeld', 'link-1');">PlotMeld</a></tt> <tt class="py-keyword">as</tt> <tt class="py-name">PM</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Package BIP=BIP-module.html"><a title="BIP" class="py-name" href="#" onclick="return doclink('link-2', 'BIP', 'link-2');">BIP</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Variable BIP.Bayes.Melding.Viz=BIP.Bayes.Melding-module.html#Viz,Package BIP.Viz=BIP.Viz-module.html"><a title="BIP.Bayes.Melding.Viz
BIP.Viz" class="py-name" href="#" onclick="return doclink('link-3', 'Viz', 'link-3');">Viz</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module BIP.Viz.realtime=BIP.Viz.realtime-module.html"><a title="BIP.Viz.realtime" class="py-name" href="#" onclick="return doclink('link-4', 'realtime', 'link-4');">realtime</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class BIP.Viz.realtime.RTplot=BIP.Viz.realtime.RTplot-class.html"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-5', 'RTplot', 'link-5');">RTplot</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt id="link-6" class="py-name"><a title="BIP.Bayes.Melding.Viz
BIP.Viz" class="py-name" href="#" onclick="return doclink('link-6', 'Viz', 'link-3');">Viz</a></tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt id="link-7" class="py-name"><a title="BIP.Bayes.Melding.Viz
BIP.Viz" class="py-name" href="#" onclick="return doclink('link-7', 'Viz', 'link-3');">Viz</a></tt><tt class="py-op">=</tt><tt class="py-name">False</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">r"""Please install Gnuplot-py to enable realtime visualization.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-string">    http://gnuplot-py.sourceforge.net/</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-string">    """</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Module BIP.Bayes.lhs=BIP.Bayes.lhs-module.html,Function BIP.Bayes.lhs.lhs()=BIP.Bayes.lhs-module.html#lhs"><a title="BIP.Bayes.lhs
BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-8', 'lhs', 'link-8');">lhs</a></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">multiprocessing</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Pool</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt id="link-9" class="py-name"><a title="BIP.Bayes.Melding.Viz
BIP.Viz" class="py-name" href="#" onclick="return doclink('link-9', 'Viz', 'link-3');">Viz</a></tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">    <tt id="link-10" class="py-name" targets="Variable BIP.Bayes.Melding.dtplot=BIP.Bayes.Melding-module.html#dtplot"><a title="BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-10', 'dtplot', 'link-10');">dtplot</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-11', 'RTplot', 'link-5');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-12" class="py-name" targets="Variable BIP.Bayes.Melding.phiplot=BIP.Bayes.Melding-module.html#phiplot"><a title="BIP.Bayes.Melding.phiplot" class="py-name" href="#" onclick="return doclink('link-12', 'phiplot', 'link-12');">phiplot</a></tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-13', 'RTplot', 'link-5');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-14" class="py-name" targets="Variable BIP.Bayes.Melding.thplot=BIP.Bayes.Melding-module.html#thplot"><a title="BIP.Bayes.Melding.thplot" class="py-name" href="#" onclick="return doclink('link-14', 'thplot', 'link-14');">thplot</a></tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-15', 'RTplot', 'link-5');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"> </tt>
<a name="FitModel"></a><div id="FitModel-def"><a name="L49"></a><tt class="py-lineno"> 49</tt> <a class="py-toggle" href="#" id="FitModel-toggle" onclick="return toggle('FitModel');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html">FitModel</a><tt class="py-op">:</tt> </tt>
</div><div id="FitModel-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FitModel-expanded"><a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">    Fit a model to data generating</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">    Bayesian posterior distributions of input and</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-docstring">    outputs of the model.</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="FitModel.__init__"></a><div id="FitModel.__init__-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="FitModel.__init__-toggle" onclick="return toggle('FitModel.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">K</tt><tt class="py-op">,</tt><tt class="py-param">L</tt><tt class="py-op">,</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">ntheta</tt><tt class="py-op">,</tt> <tt class="py-param">nphi</tt><tt class="py-op">,</tt><tt class="py-param">inits</tt><tt class="py-op">,</tt><tt class="py-param">tf</tt><tt class="py-op">,</tt><tt class="py-param">phinames</tt><tt class="py-op">,</tt><tt class="py-param">thetanames</tt><tt class="py-op">,</tt><tt class="py-param">wl</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">nw</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-param">verbose</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel.__init__-expanded"><a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-docstring">        Initialize the model fitter.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-docstring">            - `K`: Number of samples from the priors. On MCMC also the number of samples of the posterior.</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-docstring">            - `L`: Number of samples of the posteriors. Only used on SIR and ABC methods.</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-docstring">            - `model`: Callable (function) returning the output of the model, from a set of parameter values received as argument.</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring">            - `ntheta`: Number of parameters included in the inference.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-docstring">            - `nphi`: Number of outputs of the model.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">            - `inits`: inits initial values for the model's variables.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">            - `tf`: Length of the simulation, in units of time.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">            - `phinames`: List of names (strings) with names of the model's variables</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">            - `thetanames`: List of names (strings) with names of parameters included on the inference.</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">            - `wl`: window lenght length of the inference window.</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">            - `nw`: Number of windows to analyze on iterative inference mode</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">            - `verbose`: Verbose output if True.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Class BIP.Bayes.Melding.Meld=BIP.Bayes.Melding.Meld-class.html"><a title="BIP.Bayes.Melding.Meld" class="py-name" href="#" onclick="return doclink('link-16', 'Meld', 'link-16');">Meld</a></tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">=</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">L</tt><tt class="py-op">=</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt id="link-17" class="py-name" targets="Function BIP.Bayes.Melding.model()=BIP.Bayes.Melding-module.html#model"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-17', 'model', 'link-17');">model</a></tt><tt class="py-op">=</tt><tt id="link-18" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-18', 'model', 'link-17');">model</a></tt><tt class="py-op">,</tt><tt class="py-name">ntheta</tt><tt class="py-op">=</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-name">nphi</tt><tt class="py-op">=</tt><tt class="py-number">5</tt><tt class="py-op">,</tt><tt class="py-name">verbose</tt><tt class="py-op">=</tt><tt class="py-name">verbose</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt> <tt class="py-op">=</tt> <tt class="py-name">inits</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt> <tt class="py-op">=</tt> <tt class="py-name">tf</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-19', 'model', 'link-17');">model</a></tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-20', 'model', 'link-17');">model</a></tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt> <tt class="py-op">=</tt> <tt class="py-name">nphi</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt> <tt class="py-op">=</tt> <tt class="py-name">ntheta</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt> <tt class="py-op">=</tt> <tt class="py-name">phinames</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt> <tt class="py-op">=</tt> <tt class="py-name">thetanames</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt> <tt class="py-op">=</tt> <tt class="py-name">wl</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt> <tt class="py-op">=</tt> <tt class="py-name">nw</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prior_set</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">         </tt>
<a name="FitModel.set_priors"></a><div id="FitModel.set_priors-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="FitModel.set_priors-toggle" onclick="return toggle('FitModel.set_priors');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#set_priors">set_priors</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">pdists</tt><tt class="py-op">,</tt><tt class="py-param">ppars</tt><tt class="py-op">,</tt><tt class="py-param">tdists</tt><tt class="py-op">,</tt><tt class="py-param">tpars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.set_priors-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel.set_priors-expanded"><a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"><tt class="py-docstring">        Set the prior distributions for Phi and Theta</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-docstring">            - `pdists`: distributions for the output variables. For example: [scipy.stats.uniform,scipy.stats.norm]</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring">            - `ppars`: paramenters for the distributions in pdists. For example: [(0,1),(0,1)]</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring">            - `tdists`: same as pdists, but for input parameters (Theta).</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">            - `tpars`: same as ppars, but for tdists.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdists</tt> <tt class="py-op">=</tt> <tt class="py-name">pdists</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ppars</tt> <tt class="py-op">=</tt> <tt class="py-name">ppars</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tdists</tt> <tt class="py-op">=</tt> <tt class="py-name">tdists</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tpars</tt> <tt class="py-op">=</tt> <tt class="py-name">tpars</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prior_set</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">     </tt>
<a name="FitModel._init_priors"></a><div id="FitModel._init_priors-def"><a name="L102"></a><tt class="py-lineno">102</tt> <a class="py-toggle" href="#" id="FitModel._init_priors-toggle" onclick="return toggle('FitModel._init_priors');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#_init_priors">_init_priors</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._init_priors-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel._init_priors-expanded"><a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'phi'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method BIP.Bayes.Melding.Meld.setThetaFromData()=BIP.Bayes.Melding.Meld-class.html#setThetaFromData"><a title="BIP.Bayes.Melding.Meld.setThetaFromData" class="py-name" href="#" onclick="return doclink('link-21', 'setThetaFromData', 'link-21');">setThetaFromData</a></tt><tt class="py-op">(</tt><tt class="py-name">names_theta</tt><tt class="py-op">,</tt><tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">.9</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">.0001</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method BIP.Bayes.Melding.Meld.setPhiFromData()=BIP.Bayes.Melding.Meld-class.html#setPhiFromData"><a title="BIP.Bayes.Melding.Meld.setPhiFromData" class="py-name" href="#" onclick="return doclink('link-22', 'setPhiFromData', 'link-22');">setPhiFromData</a></tt><tt class="py-op">(</tt><tt class="py-name">names_phi</tt><tt class="py-op">,</tt><tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'phi'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"++++&gt;"</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method BIP.Bayes.Melding.Meld.setTheta()=BIP.Bayes.Melding.Meld-class.html#setTheta"><a title="BIP.Bayes.Melding.Meld.setTheta" class="py-name" href="#" onclick="return doclink('link-23', 'setTheta', 'link-23');">setTheta</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nt</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0.001</tt><tt class="py-op">,</tt><tt class="py-number">.2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">.0001</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0.1</tt><tt class="py-op">,</tt><tt class="py-number">.5</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method BIP.Bayes.Melding.Meld.setPhi()=BIP.Bayes.Melding.Meld-class.html#setPhi"><a title="BIP.Bayes.Melding.Meld.setPhi" class="py-name" href="#" onclick="return doclink('link-24', 'setPhi', 'link-24');">setPhi</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phinames</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">np</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> </tt>
</div><a name="FitModel.do_inference"></a><div id="FitModel.do_inference-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="FitModel.do_inference-toggle" onclick="return toggle('FitModel.do_inference');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#do_inference">do_inference</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">predlen</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.do_inference-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel.do_inference-expanded"><a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method BIP.Bayes.Melding.FitModel._init_priors()=BIP.Bayes.Melding.FitModel-class.html#_init_priors"><a title="BIP.Bayes.Melding.FitModel._init_priors" class="py-name" href="#" onclick="return doclink('link-25', '_init_priors', 'link-25');">_init_priors</a></tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-name">succ</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-name">att</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"SIR"</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">succ</tt><tt class="py-op">:</tt> <tt class="py-comment">#run sir Until is able to get a fit</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'attempt #'</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">                <tt class="py-name">succ</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method BIP.Bayes.Melding.Meld.sir()=BIP.Bayes.Melding.Meld-class.html#sir"><a title="BIP.Bayes.Melding.Meld.sir" class="py-name" href="#" onclick="return doclink('link-26', 'sir', 'link-26');">sir</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">variance</tt><tt class="py-op">=</tt><tt class="py-number">1e-6</tt><tt class="py-op">,</tt><tt class="py-name">nopool</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">                <tt class="py-name">att</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">            <tt id="link-27" class="py-name" targets="Variable BIP.SDE.example.pt=BIP.SDE.example-module.html#pt"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-27', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method BIP.Bayes.Melding.Meld.getPosteriors()=BIP.Bayes.Melding.Meld-class.html#getPosteriors"><a title="BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-28', 'getPosteriors', 'link-28');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"MCMC"</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">succ</tt><tt class="py-op">:</tt> <tt class="py-comment">#run sir Until is able to get a fitd == "mcmc":</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'attempt #'</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">                <tt class="py-name">succ</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method BIP.Bayes.Melding.Meld.mcmc_run()=BIP.Bayes.Melding.Meld-class.html#mcmc_run"><a title="BIP.Bayes.Melding.Meld.mcmc_run" class="py-name" href="#" onclick="return doclink('link-29', 'mcmc_run', 'link-29');">mcmc_run</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">tf</tt><tt class="py-op">,</tt><tt class="py-name">likvariance</tt><tt class="py-op">=</tt><tt class="py-number">.5e-7</tt><tt class="py-op">,</tt><tt class="py-name">burnin</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">            <tt id="link-30" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-30', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-31', 'getPosteriors', 'link-28');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"ABC"</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">            <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method BIP.Bayes.Melding.Meld.abcRun()=BIP.Bayes.Melding.Meld-class.html#abcRun"><a title="BIP.Bayes.Melding.Meld.abcRun" class="py-name" href="#" onclick="return doclink('link-32', 'abcRun', 'link-32');">abcRun</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">fitfun</tt><tt class="py-op">=</tt><tt class="py-name">fitInc</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-number">105</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">            <tt id="link-33" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-33', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-34', 'getPosteriors', 'link-28');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">tf</tt><tt class="py-op">)</tt> </tt>
</div><a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"> </tt>
<a name="FitModel.run"></a><div id="FitModel.run-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="FitModel.run-toggle" onclick="return toggle('FitModel.run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">method</tt><tt class="py-op">,</tt><tt class="py-param">monitor</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.run-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel.run-expanded"><a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-docstring">        Fit the model against data</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: dictionary with variable names and observed series, as Key and value respectively.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-docstring">            - `method`: Inference method: "ABC", "SIR" or "MCMC"</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prior_set</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">monitor</tt><tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method BIP.Bayes.Melding.FitModel._monitor_setup()=BIP.Bayes.Melding.FitModel-class.html#_monitor_setup"><a title="BIP.Bayes.Melding.FitModel._monitor_setup" class="py-name" href="#" onclick="return doclink('link-35', '_monitor_setup', 'link-35');">_monitor_setup</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">        <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'theta'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'phi'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">        <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt class="py-string">'rm wres_*'</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">        <tt class="py-name">wl</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wl</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">w</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; Window # %s of %s!'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">,</tt><tt class="py-name">nw</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tf</tt><tt class="py-op">=</tt><tt class="py-name">wl</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">            <tt class="py-name">d2</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-comment">#Slicing data to the current window</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">                <tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">v</tt><tt class="py-op">[</tt><tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">wl</tt><tt class="py-op">:</tt><tt class="py-name">w</tt><tt class="py-op">*</tt><tt class="py-name">wl</tt><tt class="py-op">+</tt><tt class="py-name">wl</tt><tt class="py-op">]</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-name">v</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">w</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-string">'I'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">)</tt> <tt class="py-comment">#adjusting sunceptibles</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">            <tt id="link-36" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-36', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">att</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method BIP.Bayes.Melding.FitModel.do_inference()=BIP.Bayes.Melding.FitModel-class.html#do_inference"><a title="BIP.Bayes.Melding.FitModel.do_inference" class="py-name" href="#" onclick="return doclink('link-37', 'do_inference', 'link-37');">do_inference</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">d2</tt><tt class="py-op">,</tt> <tt class="py-name">prior</tt><tt class="py-op">=</tt><tt class="py-name">prior</tt><tt class="py-op">,</tt><tt class="py-name">predlen</tt><tt class="py-op">=</tt><tt class="py-name">wl</tt><tt class="py-op">,</tt> <tt class="py-name">method</tt><tt class="py-op">=</tt><tt class="py-name">method</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">            <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'wres_%s'</tt><tt class="py-op">%</tt><tt class="py-name">w</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">            <tt class="py-comment">#save weekly posteriors of theta and phi, posteriors of series, data (d) and predictions(z)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">            <tt class="py-name">cPickle</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-38', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt> <tt class="py-name">att</tt><tt class="py-op">*</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">            <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'theta'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'phi'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-39" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-39', 'pt', 'link-27');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">                <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-40', 'pt', 'link-27');">pt</a></tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">            <tt class="py-comment">#beta,alpha,sigma,Ri  = median(pt.beta),median(pt.alpha),median(pt.sigma),median(pt.Ri</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">                <tt class="py-comment">#print compress(isinf(pp[n]),pp[n])</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">                <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'phi'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">monitor</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method BIP.Bayes.Melding.FitModel._monitor_plot()=BIP.Bayes.Melding.FitModel-class.html#_monitor_plot"><a title="BIP.Bayes.Melding.FitModel._monitor_plot" class="py-name" href="#" onclick="return doclink('link-41', '_monitor_plot', 'link-41');">_monitor_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">prior</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"time: %s seconds"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">start</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"> </tt>
<a name="FitModel._monitor_setup"></a><div id="FitModel._monitor_setup-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="FitModel._monitor_setup-toggle" onclick="return toggle('FitModel._monitor_setup');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#_monitor_setup">_monitor_setup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._monitor_setup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel._monitor_setup-expanded"><a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"><tt class="py-docstring">        Sets up realtime plotting of inference</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hst</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-42', 'RTplot', 'link-5');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#realtime display of theta histograms</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hsp</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-43', 'RTplot', 'link-5');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-comment">#realtime display of phi histograms</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Variable BIP.SDE.gillespie.ser=BIP.SDE.gillespie-module.html#ser"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-44', 'ser', 'link-44');">ser</a></tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-45', 'RTplot', 'link-5');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-comment">#realtime display of phi time series</tt> </tt>
</div><a name="FitModel._monitor_plot"></a><div id="FitModel._monitor_plot-def"><a name="L185"></a><tt class="py-lineno">185</tt> <a class="py-toggle" href="#" id="FitModel._monitor_plot-toggle" onclick="return toggle('FitModel._monitor_plot');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#_monitor_plot">_monitor_plot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">series</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._monitor_plot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel._monitor_plot-expanded"><a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"><tt class="py-docstring">        Plots real time data</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-46', 'ser', 'link-44');">ser</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method BIP.Viz.realtime.RTplot.plotlines()=BIP.Viz.realtime.RTplot-class.html#plotlines"><a title="BIP.Viz.realtime.RTplot.plotlines" class="py-name" href="#" onclick="return doclink('link-47', 'plotlines', 'link-47');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-string">r'I'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-string">'points'</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'Obs. I'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-name">i5</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">2.5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-string">r'I'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-name">i95</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">97.5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-string">r'I'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-name">diff</tt> <tt class="py-op">=</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">I</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">[</tt><tt class="py-string">'I'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt class="py-name">initind</tt> <tt class="py-op">=</tt> <tt class="py-name">diff</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">diff</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-48', 'ser', 'link-44');">ser</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="BIP.Viz.realtime.RTplot.plotlines" class="py-name" href="#" onclick="return doclink('link-49', 'plotlines', 'link-47');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-string">r'I'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">initind</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">"Best run's I"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-50', 'ser', 'link-44');">ser</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="BIP.Viz.realtime.RTplot.plotlines" class="py-name" href="#" onclick="return doclink('link-51', 'plotlines', 'link-47');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">i5</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'2.5%'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-52', 'ser', 'link-44');">ser</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="BIP.Viz.realtime.RTplot.plotlines" class="py-name" href="#" onclick="return doclink('link-53', 'plotlines', 'link-47');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">i95</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'97.5%'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'Week %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hst</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method BIP.Viz.realtime.RTplot.plothist()=BIP.Viz.realtime.RTplot-class.html#plothist"><a title="BIP.Viz.realtime.RTplot.plothist" class="py-name" href="#" onclick="return doclink('link-54', 'plothist', 'link-54');">plothist</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-string">'theta'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetanames</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'Week %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-55', 'ser', 'link-44');">ser</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method BIP.Viz.realtime.RTplot.clearFig()=BIP.Viz.realtime.RTplot-class.html#clearFig"><a title="BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-56', 'clearFig', 'link-56');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hst</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-57', 'clearFig', 'link-56');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hsp</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-58', 'clearFig', 'link-56');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">     </tt>
<a name="FitModel.plot_results"></a><div id="FitModel.plot_results-def"><a name="L202"></a><tt class="py-lineno">202</tt> <a class="py-toggle" href="#" id="FitModel.plot_results-toggle" onclick="return toggle('FitModel.plot_results');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#plot_results">plot_results</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel.plot_results-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel.plot_results-expanded"><a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"><tt class="py-docstring">        Plot the final results of the inference</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">        <tt id="link-59" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-59', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name" targets="Method BIP.Bayes.Melding.FitModel._read_results()=BIP.Bayes.Melding.FitModel-class.html#_read_results"><a title="BIP.Bayes.Melding.FitModel._read_results" class="py-name" href="#" onclick="return doclink('link-60', '_read_results', 'link-60');">_read_results</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">        <tt class="py-name">PM</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Function BIP.Bayes.PlotMeld.plot_par_series()=BIP.Bayes.PlotMeld-module.html#plot_par_series"><a title="BIP.Bayes.PlotMeld.plot_par_series" class="py-name" href="#" onclick="return doclink('link-61', 'plot_par_series', 'link-61');">plot_par_series</a></tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-62', 'pt', 'link-27');">pt</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-63" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-63', 'pt', 'link-27');">pt</a></tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">        <tt class="py-name">PM</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Function BIP.Bayes.PlotMeld.plot_par_violin()=BIP.Bayes.PlotMeld-module.html#plot_par_violin"><a title="BIP.Bayes.PlotMeld.plot_par_violin" class="py-name" href="#" onclick="return doclink('link-64', 'plot_par_violin', 'link-64');">plot_par_violin</a></tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-65', 'pt', 'link-27');">pt</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-66" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-66', 'pt', 'link-27');">pt</a></tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-name">PM</tt><tt class="py-op">.</tt><tt class="py-name">predNewCases</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">nc</tt><tt class="py-op">,</tt><tt class="py-name">fig</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">ws</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">        <tt id="link-67" class="py-name" targets="Function BIP.Bayes.PlotMeld.plot_series2()=BIP.Bayes.PlotMeld-module.html#plot_series2"><a title="BIP.Bayes.PlotMeld.plot_series2" class="py-name" href="#" onclick="return doclink('link-67', 'plot_series2', 'link-67');">plot_series2</a></tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">nc</tt><tt class="py-op">*</tt><tt class="py-name">ws</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt id="link-68" class="py-name"><a title="BIP.Bayes.PlotMeld.plot_series2" class="py-name" href="#" onclick="return doclink('link-68', 'plot_series2', 'link-67');">plot_series2</a></tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">nc</tt><tt class="py-op">*</tt><tt class="py-name">ws</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">tit</tt><tt class="py-op">=</tt><tt class="py-string">'Predicted vs. Observed series'</tt><tt class="py-op">,</tt><tt class="py-name">lag</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"> </tt>
<a name="FitModel._read_results"></a><div id="FitModel._read_results-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="FitModel._read_results-toggle" onclick="return toggle('FitModel._read_results');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.FitModel-class.html#_read_results">_read_results</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FitModel._read_results-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FitModel._read_results-expanded"><a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"><tt class="py-docstring">        read results from disk</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">        <tt id="link-69" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-69', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">w</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nw</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">            <tt class="py-name">fn</tt> <tt class="py-op">=</tt> <tt class="py-string">'wres_%s'</tt><tt class="py-op">%</tt><tt class="py-name">w</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-name">fn</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">            <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fn</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">            <tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-name">pred</tt><tt class="py-op">,</tt> <tt class="py-name">samples</tt> <tt class="py-op">=</tt> <tt class="py-name">cPickle</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">            <tt id="link-70" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-70', 'pt', 'link-27');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">            <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">            <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">            <tt class="py-name">predseries</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pred</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-71" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-71', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">predseries</tt> </tt>
</div></div><a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">             </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"> </tt>
<a name="Meld"></a><div id="Meld-def"><a name="L236"></a><tt class="py-lineno">236</tt> <a class="py-toggle" href="#" id="Meld-toggle" onclick="return toggle('Meld');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html">Meld</a><tt class="py-op">:</tt> </tt>
</div><div id="Meld-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Meld-expanded"><a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"><tt class="py-docstring">    Bayesian Melding class</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="Meld.__init__"></a><div id="Meld.__init__-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="Meld.__init__-toggle" onclick="return toggle('Meld.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt>  <tt class="py-param">K</tt><tt class="py-op">,</tt>  <tt class="py-param">L</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">ntheta</tt><tt class="py-op">,</tt> <tt class="py-param">nphi</tt><tt class="py-op">,</tt> <tt class="py-param">alpha</tt> <tt class="py-op">=</tt> <tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-param">verbose</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">viz</tt><tt class="py-op">=</tt><tt class="py-name">False</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.__init__-expanded"><a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"><tt class="py-docstring">        Initializes the Melding class.</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"><tt class="py-docstring">            - `K`: Number of replicates of the model run. Also determines the prior sample size.</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line"><tt class="py-docstring">            - `L`: Number of samples from the Posterior distributions. Usually 10% of K.</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line"><tt class="py-docstring">            - `model`: Callable taking theta as argument and returning phi = M(theta).</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line"><tt class="py-docstring">            - `ntheta`: Number of inputs to the model (parameters).</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line"><tt class="py-docstring">            - `nphi`: Number of outputs of the model (State-variables)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line"><tt class="py-docstring">            - `verbose`: Boolean: whether to show more information about the computations</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line"><tt class="py-docstring">            - `viz`: Boolean. Wether to show graphical outputs of the fitting process</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt> <tt class="py-op">=</tt> <tt class="py-name">K</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt> <tt class="py-op">=</tt> <tt class="py-name">L</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt> <tt class="py-op">=</tt> <tt class="py-name">verbose</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-72', 'model', 'link-17');">model</a></tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-73', 'model', 'link-17');">model</a></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likelist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment">#list of likelihoods</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">ntheta</tt><tt class="py-op">)</tt> <tt class="py-comment">#Theta Priors (record array)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">ntheta</tt><tt class="py-op">)</tt> <tt class="py-comment">#Theta Posteriors (record array)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> <tt class="py-comment">#Phi Priors (record array)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> <tt class="py-comment">#Phi model-induced Priors (record array)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2type</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment">#list of distribution types</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> <tt class="py-comment">#Phi Posteriors (record array)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt> <tt class="py-op">=</tt> <tt class="py-name">ntheta</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt> <tt class="py-op">=</tt> <tt class="py-name">nphi</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetapars</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phipars</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-name">alpha</tt> <tt class="py-comment">#pooling weight of user-provided phi priors</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-comment">#parameterized rngs for each parameter</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi_dists</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-comment">#parameterized rngs for each variable</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">proposal_variance</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0000001</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-comment">#adaptive variance. Used my metropolis hastings</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">=</tt> <tt class="py-number">0.1</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-74" class="py-name"><a title="BIP.Bayes.Melding.Viz
BIP.Viz" class="py-name" href="#" onclick="return doclink('link-74', 'Viz', 'link-3');">Viz</a></tt><tt class="py-op">:</tt> <tt class="py-comment">#Gnuplot installed</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">viz</tt> <tt class="py-op">=</tt> <tt class="py-name">viz</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">viz</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"><tt class="py-comment">#        self.po = Pool() #pool of processes for parallel processing</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">     </tt>
<a name="Meld.setPhi"></a><div id="Meld.setPhi-def"><a name="L281"></a><tt class="py-lineno">281</tt> <a class="py-toggle" href="#" id="Meld.setPhi-toggle" onclick="return toggle('Meld.setPhi');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#setPhi">setPhi</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">,</tt> <tt class="py-param">dists</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">norm</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">limits</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setPhi-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.setPhi-expanded"><a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the models Outputs, or Phi, and generate the samples from prior distributions </tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line"><tt class="py-docstring">        needed for the melding replicates.</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the variables.</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line"><tt class="py-docstring">            - `dists`: is a list of RNG from scipy.stats</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"><tt class="py-docstring">            - `pars`: is a list of tuples of variables for each prior distribution, respectively.</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: lower and upper limits on the support of variables.</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Number of names(%s) does not match the number of output variables(%s)."</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plimits</tt> <tt class="py-op">=</tt> <tt class="py-name">limits</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phipars</tt> <tt class="py-op">=</tt> <tt class="py-name">pars</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">dists</tt><tt class="py-op">,</tt><tt class="py-name">pars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-75" class="py-name"><a title="BIP.Bayes.lhs
BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-75', 'lhs', 'link-8');">lhs</a></tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="BIP.Bayes.lhs
BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-76', 'lhs', 'link-8');">lhs</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2type</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">)</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi_dists</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">d</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> </tt>
</div><a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">         </tt>
<a name="Meld.setTheta"></a><div id="Meld.setTheta-def"><a name="L306"></a><tt class="py-lineno">306</tt> <a class="py-toggle" href="#" id="Meld.setTheta-toggle" onclick="return toggle('Meld.setTheta');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#setTheta">setTheta</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">,</tt> <tt class="py-param">dists</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">norm</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setTheta-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.setTheta-expanded"><a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the models inputs and generate the samples from prior distributions </tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"><tt class="py-docstring">        needed for the dists the melding replicates.</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the parameters.</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line"><tt class="py-docstring">            - `dists`: is a list of RNG from scipy.stats</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line"><tt class="py-docstring">            - `pars`: is a list of tuples of parameters for each prior distribution, respectivelydists</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">thetapars</tt> <tt class="py-op">=</tt> <tt class="py-name">pars</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt> <tt class="py-op">=</tt> <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">dists</tt><tt class="py-op">,</tt><tt class="py-name">pars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-77" class="py-name"><a title="BIP.Bayes.lhs
BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-77', 'lhs', 'link-8');">lhs</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="BIP.Bayes.lhs
BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-78', 'lhs', 'link-8');">lhs</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">d</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt> </tt>
</div><a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">         </tt>
<a name="Meld.add_salt"></a><div id="Meld.add_salt-def"><a name="L326"></a><tt class="py-lineno">326</tt> <a class="py-toggle" href="#" id="Meld.add_salt-toggle" onclick="return toggle('Meld.add_salt');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#add_salt">add_salt</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">dataset</tt><tt class="py-op">,</tt><tt class="py-param">band</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.add_salt-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.add_salt-expanded"><a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line"><tt class="py-docstring">        Adds a few extra uniformly distributed data </tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line"><tt class="py-docstring">        points beyond the dataset range.</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line"><tt class="py-docstring">        This is done by adding from a uniform dist.</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line"><tt class="py-docstring">            - `dataset`: vector of data</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line"><tt class="py-docstring">            - `band`: Fraction of range to extend [0,1[</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line"><tt class="py-docstring">            </tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line"><tt class="py-docstring">            Salted dataset.</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">        <tt class="py-name">dmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">        <tt class="py-name">dmin</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">        <tt class="py-name">drange</tt> <tt class="py-op">=</tt> <tt class="py-name">dmax</tt><tt class="py-op">-</tt><tt class="py-name">dmin</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">        <tt class="py-name">hb</tt> <tt class="py-op">=</tt> <tt class="py-name">drange</tt><tt class="py-op">*</tt><tt class="py-name">band</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">        <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">concatenate</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">,</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">(</tt><tt class="py-name">dmin</tt><tt class="py-op">-</tt><tt class="py-name">hb</tt><tt class="py-op">,</tt><tt class="py-name">dmax</tt><tt class="py-op">-</tt><tt class="py-name">dmin</tt><tt class="py-op">+</tt><tt class="py-name">hb</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">*</tt><tt class="py-number">.05</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">d</tt> </tt>
</div><a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">     </tt>
<a name="Meld.setThetaFromData"></a><div id="Meld.setThetaFromData-def"><a name="L346"></a><tt class="py-lineno">346</tt> <a class="py-toggle" href="#" id="Meld.setThetaFromData-toggle" onclick="return toggle('Meld.setThetaFromData');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#setThetaFromData">setThetaFromData</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setThetaFromData-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.setThetaFromData-expanded"><a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the model inputs and set the prior distributions from the vectors</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line"><tt class="py-docstring">        in data.</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line"><tt class="py-docstring">        This method is to be used when the prior distributions are available in </tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line"><tt class="py-docstring">        the form of a sample from an empirical distribution such as a bayesian</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line"><tt class="py-docstring">        posterior.</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line"><tt class="py-docstring">        In order to expand the samples provided, K samples are generated from a</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line"><tt class="py-docstring">        kernel density estimate of the original sample.</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the parameters.</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: list of vectors. Samples of a proposed distribution</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: List of (min,max) tuples for each theta to make sure samples are not generated outside these limits.</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">        <tt class="py-name">tlimits</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">limits</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">        <tt class="py-keyword">class</tt> <tt class="py-def-name">Proposal</tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">__init__</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">dist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt> <tt class="py-op">=</tt> <tt class="py-name">name</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">dist</tt> </tt>
</div><a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">            <tt class="py-keyword">def</tt> <tt class="py-def-name">__call__</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">                <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">                <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">&gt;=</tt><tt class="py-name">tlimits</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">smp</tt><tt class="py-op">&lt;=</tt><tt class="py-name">tlimits</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">smp</tt> </tt>
</div></div><a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">                 </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt> <tt class="py-op">=</tt> <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">lim</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">                <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">                <tt class="py-comment">#add some points uniformly across the support </tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line">                <tt class="py-comment">#to help MCMC to escape from prior bounds</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line">                <tt class="py-name">salted</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name" targets="Method BIP.Bayes.Melding.Meld.add_salt()=BIP.Bayes.Melding.Meld-class.html#add_salt,Method BIP.Bayes.Samplers.MCMC.Metropolis.add_salt()=BIP.Bayes.Samplers.MCMC.Metropolis-class.html#add_salt"><a title="BIP.Bayes.Melding.Meld.add_salt
BIP.Bayes.Samplers.MCMC.Metropolis.add_salt" class="py-name" href="#" onclick="return doclink('link-79', 'add_salt', 'link-79');">add_salt</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line"> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">                <tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">salted</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">                <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">:</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">x</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">lim</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">x</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">lim</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">                <tt class="py-comment">#print self.q1theta[n].shape, array(smp[:self.K]).shape</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">Proposal</tt><tt class="py-op">(</tt><tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">dist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line"> </tt>
<a name="Meld.setPhiFromData"></a><div id="Meld.setPhiFromData-def"><a name="L390"></a><tt class="py-lineno">390</tt> <a class="py-toggle" href="#" id="Meld.setPhiFromData-toggle" onclick="return toggle('Meld.setPhiFromData');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#setPhiFromData">setPhiFromData</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.setPhiFromData-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.setPhiFromData-expanded"><a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line"><tt class="py-docstring">        Setup the model outputs and set their prior distributions from the</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line"><tt class="py-docstring">        vectors in data.</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line"><tt class="py-docstring">        This method is to be used when the prior distributions are available in</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line"><tt class="py-docstring">        the form of a sample from an empirical distribution such as a bayesian</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line"><tt class="py-docstring">        posterior.</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line"><tt class="py-docstring">        In order to expand the samples provided, K samples are generated from a</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line"><tt class="py-docstring">        kernel density estimate of the original sample.</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line"><tt class="py-docstring">            - `names`: list of string with the names of the variables.</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: list of vectors. Samples of the proposed distribution.</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: list of tuples (ll,ul),lower and upper limits on the support of variables.</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">names</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">limits</tt> <tt class="py-op">=</tt> <tt class="py-name">limits</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">            <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">:</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line">                <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">x</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">limits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">x</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">limits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line">                <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">                    <tt class="py-comment">#d is has no variation, i.e., all elements are the same</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">                    <tt class="py-comment">#print d</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line">                    <tt class="py-comment">#raise LinAlgError, "Singular matrix"</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line">                    <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">d</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-comment">#in this case return a constant sample</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">smp</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2type</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">'empirical'</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">        <tt class="py-comment">#self.q2phi = self.filtM(self.q2phi, self.q2phi, limits)</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line"> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">         </tt>
<a name="Meld.run"></a><div id="Meld.run-def"><a name="L426"></a><tt class="py-lineno">426</tt> <a class="py-toggle" href="#" id="Meld.run-toggle" onclick="return toggle('Meld.run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.run-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.run-expanded"><a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line"><tt class="py-docstring">        Runs the model through the Melding inference.model</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line"><tt class="py-docstring">        model is a callable which return the output of the deterministic model,</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line"><tt class="py-docstring">        i.e. the model itself.</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt>  <tt class="py-line"><tt class="py-docstring">        The model is run self.K times to obtain phi = M(theta).</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line">         </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line">            <tt id="link-80" class="py-name" targets="Variable BIP.SDE.example.r=BIP.SDE.example-module.html#r"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-80', 'r', 'link-80');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">po</tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-81', 'model', 'link-17');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-82', 'r', 'link-80');">r</a></tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-comment">#self.model(*theta)[-1] #phi is the last point in the simulation</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line"> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">         </tt>
<a name="Meld.getPosteriors"></a><div id="Meld.getPosteriors-def"><a name="L441"></a><tt class="py-lineno">441</tt> <a class="py-toggle" href="#" id="Meld.getPosteriors-toggle" onclick="return toggle('Meld.getPosteriors');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#getPosteriors">getPosteriors</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">t</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.getPosteriors-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.getPosteriors-expanded"><a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line"><tt class="py-docstring">        Updates the posteriors of the model's output for the last t time steps.</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line"><tt class="py-docstring">        Returns two record arrays:</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line"><tt class="py-docstring">        - The posteriors of the Theta</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line"><tt class="py-docstring">        - the posterior of Phi last t values of time-series. self.L by `t` arrays.</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: length of the posterior time-series to return.</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt><tt class="py-op">:</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">cb</tt><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line">            <tt class="py-docstring">'''</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line"><tt class="py-docstring">            callback function for the asynchronous model runs.</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line"><tt class="py-docstring">            r: tuple with results of simulation (results, run#)</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line"><tt class="py-docstring">            '''</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">[</tt><tt id="link-83" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-83', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-84" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-84', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line">                <tt class="py-comment">#self.post_phi[r[1]]= [tuple(l) for l in r[0][-t:]]</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">[</tt><tt id="link-85" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-85', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt id="link-86" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-86', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">t</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
</div><a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line">        <tt class="py-name">po</tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line">        <tt class="py-comment">#random indices for the marginal posteriors of theta</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt>  <tt class="py-line">        <tt class="py-name">pti</tt> <tt class="py-op">=</tt> <tt id="link-87" class="py-name"><a title="BIP.Bayes.lhs
BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-87', 'lhs', 'link-8');">lhs</a></tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="BIP.Bayes.lhs
BIP.Bayes.lhs.lhs" class="py-name" href="#" onclick="return doclink('link-88', 'lhs', 'link-8');">lhs</a></tt><tt class="py-op">(</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">randint</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">siz</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-comment">#Monte Carlo with values of the posterior of Theta</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">pti</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt>  <tt class="py-line">            <tt class="py-name">po</tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt id="link-89" class="py-name" targets="Function BIP.Bayes.Melding.enumRun()=BIP.Bayes.Melding-module.html#enumRun"><a title="BIP.Bayes.Melding.enumRun" class="py-name" href="#" onclick="return doclink('link-89', 'enumRun', 'link-89');">enumRun</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-90', 'model', 'link-17');">model</a></tt><tt class="py-op">,</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">callback</tt><tt class="py-op">=</tt><tt class="py-name">cb</tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line"><tt class="py-comment">#            r = po.apply_async(self.model,theta)</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line"><tt class="py-comment">#            if t == 1:</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt>  <tt class="py-line"><tt class="py-comment">#                self.post_phi[i] = r.get()[-1]</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line"><tt class="py-comment">#            else:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line"><tt class="py-comment">#                self.post_phi[i]= [tuple(l) for l in r.get()[-t:]]</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; L = %s\r"</tt><tt class="py-op">%</tt><tt class="py-name">i</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line"> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt>  <tt class="py-line">        <tt class="py-name">po</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">        <tt class="py-name">po</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> </tt>
</div><a name="L483"></a><tt class="py-lineno">483</tt>  <tt class="py-line"> </tt>
<a name="Meld.filtM"></a><div id="Meld.filtM-def"><a name="L484"></a><tt class="py-lineno">484</tt> <a class="py-toggle" href="#" id="Meld.filtM-toggle" onclick="return toggle('Meld.filtM');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#filtM">filtM</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">cond</tt><tt class="py-op">,</tt><tt class="py-param">x</tt><tt class="py-op">,</tt><tt class="py-param">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.filtM-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.filtM-expanded"><a name="L485"></a><tt class="py-lineno">485</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line"><tt class="py-docstring">        Multiple condition filtering.</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line"><tt class="py-docstring">        Remove values in x[i], if corresponding values in</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line"><tt class="py-docstring">        cond[i] are less than limits[i][0] or greater than</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt>  <tt class="py-line"><tt class="py-docstring">        limits[i][1].</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line"><tt class="py-docstring">            - `cond`: is an array of conditions.</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line"><tt class="py-docstring">            - `limits`: is a list of tuples (ll,ul) with length equal to number of lines in `cond` and `x`.</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt>  <tt class="py-line"><tt class="py-docstring">            - `x`: array to be filtered.</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt>  <tt class="py-line">        <tt class="py-comment"># Deconstruct the record array, if necessary.</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">,</tt> <tt class="py-name">recarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt>  <tt class="py-line">            <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt>  <tt class="py-line">            <tt class="py-name">cond</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">cond</tt><tt class="py-op">[</tt><tt class="py-name">v</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cond</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt>  <tt class="py-line">            <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">v</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt>  <tt class="py-line"> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt>  <tt class="py-line">        <tt class="py-name">cond</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">)</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt>  <tt class="py-line">        <tt class="py-name">cnd</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">cond</tt><tt class="py-op">,</tt><tt class="py-name">limits</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt>  <tt class="py-line">            <tt class="py-name">ll</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt>  <tt class="py-line">            <tt class="py-name">ul</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt>  <tt class="py-line">            <tt class="py-comment">#print cond.shape,cnd.shape,i.shape,ll,ul</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt>  <tt class="py-line">            <tt class="py-name">cnd</tt> <tt class="py-op">=</tt> <tt class="py-name">cnd</tt> <tt class="py-op">&amp;</tt> <tt class="py-name">less</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">ul</tt><tt class="py-op">)</tt> <tt class="py-op">&amp;</tt> <tt class="py-name">greater</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">ll</tt><tt class="py-op">)</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">compress</tt><tt class="py-op">(</tt><tt class="py-name">cnd</tt><tt class="py-op">,</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt>  <tt class="py-line"> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt><tt class="py-comment">#Reconstruct the record array</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt>  <tt class="py-line">            <tt id="link-91" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-91', 'r', 'link-80');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt>  <tt class="py-line">                <tt id="link-92" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-92', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">f</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">=</tt><tt id="link-93" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-93', 'r', 'link-80');">r</a></tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt>  <tt class="py-line"> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">f</tt> </tt>
</div><a name="L519"></a><tt class="py-lineno">519</tt>  <tt class="py-line"> </tt>
<a name="Meld.basicfit"></a><div id="Meld.basicfit-def"><a name="L520"></a><tt class="py-lineno">520</tt> <a class="py-toggle" href="#" id="Meld.basicfit-toggle" onclick="return toggle('Meld.basicfit');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#basicfit">basicfit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">s1</tt><tt class="py-op">,</tt><tt class="py-param">s2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.basicfit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.basicfit-expanded"><a name="L521"></a><tt class="py-lineno">521</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt>  <tt class="py-line"><tt class="py-docstring">        Calculates a basic fitness calculation between a model-</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt>  <tt class="py-line"><tt class="py-docstring">        generated time series and a observed time series.</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt>  <tt class="py-line"><tt class="py-docstring">        it uses a normalized RMS variation.</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt>  <tt class="py-line"><tt class="py-docstring">            - `s1`: model-generated time series. record array.</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt>  <tt class="py-line"><tt class="py-docstring">            - `s2`: observed time series. dictionary with keys matching names of s1</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt>  <tt class="py-line"><tt class="py-docstring">        :Return:</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt>  <tt class="py-line"><tt class="py-docstring">            Root mean square deviation between &#180;s1&#180; and &#180;s2&#180;.</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt>  <tt class="py-line">        <tt class="py-name">fit</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">s2</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> <tt class="py-comment">#no observations for this variable</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt>  <tt class="py-line">            <tt class="py-name">e</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2.</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt>  <tt class="py-line">            <tt class="py-name">fit</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">e</tt><tt class="py-op">)</tt> <tt class="py-comment">#min to guarantee error is bounded to (0,1)</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt>  <tt class="py-line"> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">fit</tt><tt class="py-op">)</tt> <tt class="py-comment">#mean r-squared</tt> </tt>
</div><a name="L541"></a><tt class="py-lineno">541</tt>  <tt class="py-line">         </tt>
<a name="L542"></a><tt class="py-lineno">542</tt>  <tt class="py-line"> </tt>
<a name="Meld.logPooling"></a><div id="Meld.logPooling-def"><a name="L543"></a><tt class="py-lineno">543</tt> <a class="py-toggle" href="#" id="Meld.logPooling-toggle" onclick="return toggle('Meld.logPooling');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#logPooling">logPooling</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">phi</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.logPooling-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.logPooling-expanded"><a name="L544"></a><tt class="py-lineno">544</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt>  <tt class="py-line"><tt class="py-docstring">        Returns the probability associated with each phi[i]</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt>  <tt class="py-line"><tt class="py-docstring">        on the pooled pdf of phi and q2phi.</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt>  <tt class="py-line"><tt class="py-docstring">            - `phi`: prior of Phi induced by the model and q1theta.</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt>  <tt class="py-line">         </tt>
<a name="L552"></a><tt class="py-lineno">552</tt>  <tt class="py-line"><tt class="py-comment">#       Estimating the multivariate joint probability densities</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt>  <tt class="py-line">        <tt class="py-name">phidens</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt>  <tt class="py-line"> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt>  <tt class="py-line">        <tt class="py-name">q2dens</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt>  <tt class="py-line"><tt class="py-comment">#       Determining the pooled probabilities for each phi[i]</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt>  <tt class="py-line"><tt class="py-comment">#        qtilphi = zeros(self.K)</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt>  <tt class="py-line">        <tt class="py-name">lastp</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt>  <tt class="py-line"><tt class="py-comment">#        print lastp,lastp.shape</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt>  <tt class="py-line">        <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phidens</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">lastp</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">q2dens</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">lastp</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alpha</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">qtilphi</tt><tt class="py-op">/</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
</div><a name="L562"></a><tt class="py-lineno">562</tt>  <tt class="py-line"> </tt>
<a name="Meld.abcRun"></a><div id="Meld.abcRun-def"><a name="L563"></a><tt class="py-lineno">563</tt> <a class="py-toggle" href="#" id="Meld.abcRun-toggle" onclick="return toggle('Meld.abcRun');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#abcRun">abcRun</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">fitfun</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-param">nopool</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-param">savetemp</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.abcRun-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.abcRun-expanded"><a name="L564"></a><tt class="py-lineno">564</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt>  <tt class="py-line"><tt class="py-docstring">        Runs the model for inference through Approximate Bayes Computation</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt>  <tt class="py-line"><tt class="py-docstring">        techniques. This method should be used as an alternative to the sir.</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt>  <tt class="py-line"><tt class="py-docstring">             - `fitfun`: Callable which will return the goodness of fit of the model to data as a number between 0-1, with 1 meaning perfect fit</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt>  <tt class="py-line"><tt class="py-docstring">             - `t`: number of time steps to retain at the end of the of the model run for fitting purposes.</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt>  <tt class="py-line"><tt class="py-docstring">             - `data`: dict containing observed time series (lists of length t) of the state variables. This dict must have as many items the number of state variables, with labels matching variables names. Unorbserved variables must have an empty list as value.</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt>  <tt class="py-line"><tt class="py-docstring">             - `savetemp`: Should temp results be saved. Useful for long runs. Alows for resuming the simulation from last sa</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt>  <tt class="py-line">        <tt class="py-name">seed</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">fitfun</tt><tt class="py-op">:</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt>  <tt class="py-line">            <tt class="py-name">fitfun</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method BIP.Bayes.Melding.Meld.basicfit()=BIP.Bayes.Melding.Meld-class.html#basicfit"><a title="BIP.Bayes.Melding.Meld.basicfit" class="py-name" href="#" onclick="return doclink('link-94', 'basicfit', 'link-94');">basicfit</a></tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt>  <tt class="py-line">            <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">,</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt>  <tt class="py-line"><tt class="py-comment">#       Running the model ==========================</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Method BIP.Bayes.Melding.Meld.runModel()=BIP.Bayes.Melding.Meld-class.html#runModel"><a title="BIP.Bayes.Melding.Meld.runModel" class="py-name" href="#" onclick="return doclink('link-95', 'runModel', 'link-95');">runModel</a></tt><tt class="py-op">(</tt><tt class="py-name">savetemp</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt>  <tt class="py-line"> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the K replicates\n"</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt>  <tt class="py-line">        <tt class="py-comment"># Do Log Pooling</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">nopool</tt><tt class="py-op">:</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt>  <tt class="py-line">            <tt id="link-96" class="py-name" targets="Variable BIP.SDE.example.t0=BIP.SDE.example-module.html#t0"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-96', 't0', 'link-96');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name" targets="Method BIP.Bayes.Melding.Meld.logPooling()=BIP.Bayes.Melding.Meld-class.html#logPooling"><a title="BIP.Bayes.Melding.Meld.logPooling" class="py-name" href="#" onclick="return doclink('link-97', 'logPooling', 'link-97');">logPooling</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">)</tt> <tt class="py-comment">#vector with probability of each phi[i] belonging to qtilphi</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the Log Pooling (took %s seconds)\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-98" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-98', 't0', 'link-96');">t0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt>  <tt class="py-line">            <tt class="py-comment">#print 'max(qtilphi): ', max(qtilphi)</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'Pooled prior on ouputs is null, please check your priors, and try again.'</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt>  <tt class="py-line"><tt class="py-comment">#      </tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt>  <tt class="py-line"><tt class="py-comment">#        calculate weights</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">fitfun</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">/=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">w</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt>  <tt class="py-line">        <tt class="py-comment">#print "w=",w, mean(w), var(w)</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt>  <tt class="py-line"><tt class="py-comment">#        print</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt>  <tt class="py-line"><tt class="py-comment">#        print 'qtilphi=',qtilphi</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt>  <tt class="py-line">        <tt class="py-comment"># Resampling Thetas</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">qtilphi</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">/=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">'max(w): %s\nmean(w): %s\nvar(w): %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">var</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'Resampling weights are all zero, please check your model or data.'</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt>  <tt class="py-line">        <tt id="link-99" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-99', 't0', 'link-96');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt>  <tt class="py-line">        <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">:</tt> <tt class="py-comment"># Extract L samples from q1theta</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt>  <tt class="py-line">            <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">size</tt><tt class="py-op">)</tt><tt class="py-comment"># Random position of w and q1theta</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">&lt;=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-comment"># retain the sample according with resampling prob.</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt>  <tt class="py-line">                <tt class="py-name">j</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Resampling (L=%s) priors (took %s seconds)"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-100" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-100', 't0', 'link-96');">t0</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt>  <tt class="py-line"> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L623"></a><tt class="py-lineno">623</tt>  <tt class="py-line"> </tt>
<a name="Meld.imp_sample"></a><div id="Meld.imp_sample-def"><a name="L624"></a><tt class="py-lineno">624</tt> <a class="py-toggle" href="#" id="Meld.imp_sample-toggle" onclick="return toggle('Meld.imp_sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#imp_sample">imp_sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">n</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">w</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.imp_sample-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.imp_sample-expanded"><a name="L625"></a><tt class="py-lineno">625</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt>  <tt class="py-line"><tt class="py-docstring">        Importance sampling</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt>  <tt class="py-line"><tt class="py-docstring">            returns a sample of size n</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt>  <tt class="py-line">        <tt class="py-comment">#sanitizing weights</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Starting importance Sampling"</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">/=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt>  <tt class="py-line">        <tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt>  <tt class="py-line">        <tt class="py-name">k</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt>  <tt class="py-line">        <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">size</tt><tt class="py-op">)</tt><tt class="py-comment"># Random position of w</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt>  <tt class="py-line">                <tt class="py-name">smp</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt>  <tt class="py-line">                <tt class="py-name">j</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt>  <tt class="py-line">                 </tt>
<a name="L644"></a><tt class="py-lineno">644</tt>  <tt class="py-line">            <tt class="py-name">k</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Done imp samp."</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">smp</tt> </tt>
</div><a name="L647"></a><tt class="py-lineno">647</tt>  <tt class="py-line">     </tt>
<a name="Meld.mcmc_run"></a><div id="Meld.mcmc_run-def"><a name="L648"></a><tt class="py-lineno">648</tt> <a class="py-toggle" href="#" id="Meld.mcmc_run-toggle" onclick="return toggle('Meld.mcmc_run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#mcmc_run">mcmc_run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">likvariance</tt><tt class="py-op">=</tt><tt class="py-number">10</tt><tt class="py-op">,</tt><tt class="py-param">burnin</tt><tt class="py-op">=</tt><tt class="py-number">100</tt><tt class="py-op">,</tt> <tt class="py-param">nopool</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">=</tt><tt class="py-string">"MH"</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.mcmc_run-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.mcmc_run-expanded"><a name="L649"></a><tt class="py-lineno">649</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt>  <tt class="py-line"><tt class="py-docstring">        MCMC based fitting</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: observed time series on the model's output</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: length of the observed time series</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt>  <tt class="py-line"><tt class="py-docstring">            - `likvariance`: variance of the Normal likelihood function</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt>  <tt class="py-line"><tt class="py-docstring">            - `nopool`: True if no priors on the outputs are available. Leads to faster calculations</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt>  <tt class="py-line"><tt class="py-docstring">            - `method`: Step method. defaults to Metropolis hastings</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">"MH"</tt><tt class="py-op">:</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name" targets="Method BIP.Bayes.Melding.Meld.mh()=BIP.Bayes.Melding.Meld-class.html#mh"><a title="BIP.Bayes.Melding.Meld.mh" class="py-name" href="#" onclick="return doclink('link-101', 'mh', 'link-101');">mh</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt id="link-102" class="py-name"><a title="BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-102', 'like', 'link-0');">like</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Function BIP.Bayes.like.Normal()=BIP.Bayes.like-module.html#Normal"><a title="BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-103', 'Normal', 'link-103');">Normal</a></tt><tt class="py-op">,</tt><tt class="py-name">likvariance</tt><tt class="py-op">,</tt><tt class="py-name">burnin</tt><tt class="py-op">)</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt>  <tt class="py-line">            <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid MCMC method!\nTry 'MH'."</tt><tt class="py-op">)</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L666"></a><tt class="py-lineno">666</tt>  <tt class="py-line"> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt>  <tt class="py-line"> </tt>
<a name="Meld.mh"></a><div id="Meld.mh-def"><a name="L668"></a><tt class="py-lineno">668</tt> <a class="py-toggle" href="#" id="Meld.mh-toggle" onclick="return toggle('Meld.mh');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#mh">mh</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">,</tt><tt class="py-param">t</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">likfun</tt><tt class="py-op">,</tt><tt class="py-param">variance</tt><tt class="py-op">,</tt> <tt class="py-param">burnin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.mh-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.mh-expanded"><a name="L669"></a><tt class="py-lineno">669</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt>  <tt class="py-line"><tt class="py-docstring">        Simple Metropolis hastings. </tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt>  <tt class="py-line"><tt class="py-docstring">        Assumes symmetric proposal distributions.</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt>  <tt class="py-line"><tt class="py-docstring">            - `n`: number of samples to obtain</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: Length of time-series</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: Observation dictionary {'variable':[time-series]}</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt>  <tt class="py-line"><tt class="py-docstring">            - `likfun`: likelihood function to use</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt>  <tt class="py-line"><tt class="py-docstring">            - `variance`: variance of the likelihood function</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt>  <tt class="py-line"><tt class="py-docstring">            - `burnin`: number of samples to discard at the beginning of the chain.</tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">tune</tt><tt class="py-op">(</tt><tt class="py-param">ar</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">ar</tt><tt class="py-op">&lt;</tt><tt class="py-number">0.05</tt><tt class="py-op">:</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> <tt class="py-op">*=</tt> <tt class="py-number">0.5</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">ar</tt> <tt class="py-op">&lt;</tt><tt class="py-number">0.2</tt><tt class="py-op">:</tt> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> <tt class="py-op">*=</tt> <tt class="py-number">0.9</tt> </tt>
<a name="L686"></a><tt class="py-lineno">686</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">ar</tt> <tt class="py-op">&gt;</tt><tt class="py-number">0.9</tt><tt class="py-op">:</tt> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> <tt class="py-op">*=</tt> <tt class="py-number">10</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">ar</tt> <tt class="py-op">&gt;</tt><tt class="py-number">0.75</tt><tt class="py-op">:</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> <tt class="py-op">*=</tt> <tt class="py-number">2</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">ar</tt> <tt class="py-op">&gt;</tt><tt class="py-number">0.5</tt><tt class="py-op">:</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> <tt class="py-op">*=</tt> <tt class="py-number">1.1</tt> </tt>
</div><a name="L692"></a><tt class="py-lineno">692</tt>  <tt class="py-line">        <tt class="py-name">ptheta</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ntheta</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt>  <tt class="py-line">        <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">rej</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment">#total samples,accepted samples, rejected proposals</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt>  <tt class="py-line">        <tt class="py-name">last_lik</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt>  <tt class="py-line">        <tt class="py-name">liklist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt>  <tt class="py-line">            <tt class="py-comment">#generating proposals</tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt>  <tt class="py-line">            <tt class="py-name">pvar</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">proposal_variance</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptscalefactor</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">theta_dists</tt><tt class="py-op">[</tt><tt class="py-name">dist</tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">dist</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt>  <tt class="py-line">            <tt class="py-name">prop</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-104', 'model', 'link-17');">model</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt>  <tt class="py-line">                <tt class="py-name">prop</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">prop</tt><tt class="py-op">]</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt>  <tt class="py-line">            <tt class="py-comment">#calculate likelihoods</tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt>  <tt class="py-line">            <tt class="py-name">lik</tt><tt class="py-op">=</tt><tt class="py-number">0</tt>  </tt>
<a name="L705"></a><tt class="py-lineno">705</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#loop on series</tt> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">:</tt> </tt>
<a name="L707"></a><tt class="py-lineno">707</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt><tt class="py-comment">#Only calculate liks of series for which we have data</tt> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt>  <tt class="py-line">                <tt class="py-name">obs</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q2phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#Loop on time</tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt>  <tt class="py-line">                    <tt class="py-name">lik</tt> <tt class="py-op">+=</tt> <tt class="py-name">likfun</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">prop</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">variance</tt><tt class="py-op">)</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt>  <tt class="py-line">            <tt class="py-comment">#store samples</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">last_lik</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-comment">#on first sample</tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt>  <tt class="py-line">                <tt class="py-name">last_lik</tt> <tt class="py-op">=</tt> <tt class="py-name">lik</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt>  <tt class="py-line">             </tt>
<a name="L716"></a><tt class="py-lineno">716</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">-</tt><tt class="py-name">last_lik</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt> <tt class="py-name">lik</tt><tt class="py-op">-</tt><tt class="py-name">last_lik</tt><tt class="py-op">:</tt> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt>  <tt class="py-line">                    <tt class="py-name">rej</tt> <tt class="py-op">+=</tt><tt class="py-number">1</tt> <tt class="py-comment">#adjust rejection counter</tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt>  <tt class="py-line">                    <tt class="py-name">i</tt> <tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt>  <tt class="py-line">                    <tt class="py-comment">#print theta</tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">burnin</tt><tt class="py-op">:</tt><tt class="py-comment">#store only after burnin samples</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">prop</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">t</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">else</tt> <tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">point</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">point</tt> <tt class="py-keyword">in</tt> <tt class="py-name">prop</tt><tt class="py-op">]</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt>  <tt class="py-line">                <tt class="py-name">ptheta</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt>  <tt class="py-line">                <tt class="py-name">liklist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt>  <tt class="py-line">                <tt class="py-name">j</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> <tt class="py-comment">#update good sample counter </tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt>  <tt class="py-line">            <tt class="py-name">last_lik</tt> <tt class="py-op">=</tt> <tt class="py-name">lik</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt>  <tt class="py-line">            <tt class="py-name">i</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-name">n</tt> <tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt;"</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-string">"\r"</tt> </tt>
<a name="L731"></a><tt class="py-lineno">731</tt>  <tt class="py-line">             </tt>
<a name="L732"></a><tt class="py-lineno">732</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method BIP.Bayes.Melding.Meld.imp_sample()=BIP.Bayes.Melding.Meld-class.html#imp_sample"><a title="BIP.Bayes.Melding.Meld.imp_sample" class="py-name" href="#" onclick="return doclink('link-105', 'imp_sample', 'link-105');">imp_sample</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-name">ptheta</tt><tt class="py-op">,</tt><tt class="py-name">liklist</tt><tt class="py-op">)</tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt>  <tt class="py-line">        <tt class="py-name">ar</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-name">rej</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt>  </tt>
<a name="L734"></a><tt class="py-lineno">734</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">ar</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0.9</tt><tt class="py-op">:</tt> </tt>
<a name="L735"></a><tt class="py-lineno">735</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L736"></a><tt class="py-lineno">736</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">=</tt> <tt class="py-number">0.05</tt> </tt>
<a name="L737"></a><tt class="py-lineno">737</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">30</tt><tt class="py-op">:</tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">*=</tt> <tt class="py-number">10</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">ar</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0.7</tt><tt class="py-op">:</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">*=</tt> <tt class="py-number">2</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">ar</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0.4</tt><tt class="py-op">:</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">=</tt> <tt class="py-number">0.001</tt> <tt class="py-comment">#no more expansion</tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Total steps(i): "</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-string">"rej:"</tt><tt class="py-op">,</tt><tt class="py-name">rej</tt><tt class="py-op">,</tt> <tt class="py-string">"j:"</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"&gt;&gt;&gt; Salt-Band: %s"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"&gt;&gt;&gt; Acceptance rate: %s"</tt><tt class="py-op">%</tt><tt class="py-name">ar</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt>  <tt class="py-line">         </tt>
<a name="L747"></a><tt class="py-lineno">747</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L748"></a><tt class="py-lineno">748</tt>  <tt class="py-line">                 </tt>
<a name="L749"></a><tt class="py-lineno">749</tt>  <tt class="py-line"> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt>  <tt class="py-line"> </tt>
<a name="L751"></a><tt class="py-lineno">751</tt>  <tt class="py-line"> </tt>
<a name="Meld.sir"></a><div id="Meld.sir-def"><a name="L752"></a><tt class="py-lineno">752</tt> <a class="py-toggle" href="#" id="Meld.sir-toggle" onclick="return toggle('Meld.sir');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#sir">sir</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-param">variance</tt><tt class="py-op">=</tt><tt class="py-number">0.1</tt><tt class="py-op">,</tt> <tt class="py-param">nopool</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-param">savetemp</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.sir-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.sir-expanded"><a name="L753"></a><tt class="py-lineno">753</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt>  <tt class="py-line"><tt class="py-docstring">        Run the model output through the Sampling-Importance-Resampling algorithm.</tt> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt>  <tt class="py-line"><tt class="py-docstring">        Returns 1 if successful or 0 if not.</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: observed time series on the model's output</tt> </tt>
<a name="L759"></a><tt class="py-lineno">759</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: length of the observed time series</tt> </tt>
<a name="L760"></a><tt class="py-lineno">760</tt>  <tt class="py-line"><tt class="py-docstring">            - `variance`: variance of the Normal likelihood function</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt>  <tt class="py-line"><tt class="py-docstring">            - `nopool`: True if no priors on the outputs are available. Leads to faster calculations</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt>  <tt class="py-line"><tt class="py-docstring">            - `savetemp`: Boolean. create a temp file?</tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt>  <tt class="py-line">        <tt class="py-name">seed</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="BIP.Bayes.Melding.Meld.runModel" class="py-name" href="#" onclick="return doclink('link-106', 'runModel', 'link-95');">runModel</a></tt><tt class="py-op">(</tt><tt class="py-name">savetemp</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt>  <tt class="py-line">        <tt class="py-comment"># Do Log Pooling</tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">nopool</tt><tt class="py-op">:</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt>  <tt class="py-line">            <tt id="link-107" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-107', 't0', 'link-96');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="BIP.Bayes.Melding.Meld.logPooling" class="py-name" href="#" onclick="return doclink('link-108', 'logPooling', 'link-97');">logPooling</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">)</tt> <tt class="py-comment">#vector with probability of each phi[i] belonging to qtilphi</tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the Log Pooling (took %s seconds)\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-109" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-109', 't0', 'link-96');">t0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt>  <tt class="py-line">            <tt class="py-name">qtilphi</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'max(qtilphi): '</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">'Pooled prior on ouputs is null, please check your priors, and try again.'</tt> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt>  <tt class="py-line"> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt>  <tt class="py-line"><tt class="py-comment">#       Calculating the likelihood of each phi[i] considering the observed data</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt>  <tt class="py-line">        <tt class="py-name">lik</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt>  <tt class="py-line">        <tt id="link-110" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-110', 't0', 'link-96');">t0</a></tt><tt class="py-op">=</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt>  <tt class="py-line"><tt class="py-comment">#       po = Pool()</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt>  <tt class="py-line">            <tt class="py-name">l</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">list</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">:</tt>  </tt>
<a name="L787"></a><tt class="py-lineno">787</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> <tt class="py-comment">#no observations for this variable</tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt>  <tt class="py-line">                <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> <tt class="py-comment">#no observations for this variable</tt> </tt>
<a name="L790"></a><tt class="py-lineno">790</tt>  <tt class="py-line">                <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt>  <tt class="py-line"><tt class="py-comment">#                liklist=[po.apply_async(like.Normal,(data[n][m], j, tau)) for m,j in enumerate(p[i])]</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt>  <tt class="py-line"><tt class="py-comment">#                l=product([p.get() for p in liklist])</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt>  <tt class="py-line">                <tt class="py-name">l</tt> <tt class="py-op">*=</tt> <tt class="py-name">product</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt id="link-111" class="py-name"><a title="BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-111', 'like', 'link-0');">like</a></tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-112', 'Normal', 'link-103');">Normal</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">variance</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt>  <tt class="py-line">                <tt class="py-comment">#l += sum([like.Normal(data[n][m], j,1./(tau*j+.0001)) for m,j in enumerate(p[i])])</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt>  <tt class="py-line">             </tt>
<a name="L796"></a><tt class="py-lineno">796</tt>  <tt class="py-line">            <tt class="py-name">lik</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">l</tt> </tt>
<a name="L797"></a><tt class="py-lineno">797</tt>  <tt class="py-line"><tt class="py-comment">#        po.close()</tt> </tt>
<a name="L798"></a><tt class="py-lineno">798</tt>  <tt class="py-line"><tt class="py-comment">#        po.join()</tt> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">viz</tt><tt class="py-op">:</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt>  <tt class="py-line">            <tt id="link-113" class="py-name"><a title="BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-113', 'dtplot', 'link-10');">dtplot</a></tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-114', 'clearFig', 'link-56');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-115" class="py-name"><a title="BIP.Bayes.Melding.phiplot" class="py-name" href="#" onclick="return doclink('link-115', 'phiplot', 'link-12');">phiplot</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-116', 'clearFig', 'link-56');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">;</tt><tt id="link-117" class="py-name"><a title="BIP.Bayes.Melding.thplot" class="py-name" href="#" onclick="return doclink('link-117', 'thplot', 'link-14');">thplot</a></tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-118', 'clearFig', 'link-56');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt>  <tt class="py-line">            <tt id="link-119" class="py-name"><a title="BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-119', 'dtplot', 'link-10');">dtplot</a></tt><tt class="py-op">.</tt><tt class="py-name">gp</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'observed'</tt><tt class="py-op">)</tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt>  <tt class="py-line">            <tt id="link-120" class="py-name"><a title="BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-120', 'dtplot', 'link-10');">dtplot</a></tt><tt class="py-op">.</tt><tt class="py-name">gp</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'simulated'</tt><tt class="py-op">)</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt>  <tt class="py-line">            <tt class="py-name">obs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">;</tt><tt class="py-name">sim</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L805"></a><tt class="py-lineno">805</tt>  <tt class="py-line">                <tt class="py-name">obs</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt>  <tt class="py-line">                <tt class="py-name">sim</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt>  <tt class="py-line">            <tt id="link-121" class="py-name"><a title="BIP.Bayes.Melding.dtplot" class="py-name" href="#" onclick="return doclink('link-121', 'dtplot', 'link-10');">dtplot</a></tt><tt class="py-op">.</tt><tt id="link-122" class="py-name" targets="Method BIP.Viz.realtime.RTplot.scatter()=BIP.Viz.realtime.RTplot-class.html#scatter"><a title="BIP.Viz.realtime.RTplot.scatter" class="py-name" href="#" onclick="return doclink('link-122', 'scatter', 'link-122');">scatter</a></tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">sim</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'fit'</tt><tt class="py-op">)</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt>  <tt class="py-line">            <tt id="link-123" class="py-name"><a title="BIP.Bayes.Melding.phiplot" class="py-name" href="#" onclick="return doclink('link-123', 'phiplot', 'link-12');">phiplot</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="BIP.Viz.realtime.RTplot.plotlines" class="py-name" href="#" onclick="return doclink('link-124', 'plotlines', 'link-47');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">sim</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'Model Output'</tt><tt class="py-op">)</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt>  <tt class="py-line">            <tt id="link-125" class="py-name"><a title="BIP.Bayes.Melding.thplot" class="py-name" href="#" onclick="return doclink('link-125', 'thplot', 'link-14');">thplot</a></tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="BIP.Viz.realtime.RTplot.plothist" class="py-name" href="#" onclick="return doclink('link-126', 'plothist', 'link-54');">plothist</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'Input parameters'</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L810"></a><tt class="py-lineno">810</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Calculating Likelihoods (took %s seconds)"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-127" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-127', 't0', 'link-96');">t0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L811"></a><tt class="py-lineno">811</tt>  <tt class="py-line">        <tt class="py-name">lr</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L812"></a><tt class="py-lineno">812</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; Likelihood (min,mean,max,sum): '</tt><tt class="py-op">,</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
<a name="L813"></a><tt class="py-lineno">813</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Likelihood ratio of best run/worst run: %s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">lr</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L814"></a><tt class="py-lineno">814</tt>  <tt class="py-line"><tt class="py-comment">#        Calculating the weights</tt> </tt>
<a name="L815"></a><tt class="py-lineno">815</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">qtilphi</tt><tt class="py-op">*</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
<a name="L816"></a><tt class="py-lineno">816</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">/</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L817"></a><tt class="py-lineno">817</tt>  <tt class="py-line"> </tt>
<a name="L818"></a><tt class="py-lineno">818</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L819"></a><tt class="py-lineno">819</tt>  <tt class="py-line">            <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L820"></a><tt class="py-lineno">820</tt>  <tt class="py-line">            <tt id="link-128" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-128', 't0', 'link-96');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L821"></a><tt class="py-lineno">821</tt>  <tt class="py-line">            <tt class="py-name">maxw</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">minw</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-comment">#keep track of goodness of fit of phi</tt> </tt>
<a name="L822"></a><tt class="py-lineno">822</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">:</tt> <tt class="py-comment"># Extract L samples from q1theta</tt> </tt>
<a name="L823"></a><tt class="py-lineno">823</tt>  <tt class="py-line">                <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">size</tt><tt class="py-op">)</tt><tt class="py-comment"># Random position of w and q1theta</tt> </tt>
<a name="L824"></a><tt class="py-lineno">824</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">&lt;=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L825"></a><tt class="py-lineno">825</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-comment"># retain the sample according with resampling prob.</tt> </tt>
<a name="L826"></a><tt class="py-lineno">826</tt>  <tt class="py-line">                    <tt class="py-name">maxw</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">maxw</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L827"></a><tt class="py-lineno">827</tt>  <tt class="py-line">                    <tt class="py-name">minw</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">minw</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L828"></a><tt class="py-lineno">828</tt>  <tt class="py-line">                    <tt class="py-name">j</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L829"></a><tt class="py-lineno">829</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">j</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L830"></a><tt class="py-lineno">830</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-string">"of %s"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt> </tt>
<a name="L831"></a><tt class="py-lineno">831</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">done_running</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L832"></a><tt class="py-lineno">832</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Resampling (L=%s) priors (took %s seconds)"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">L</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-129" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-129', 't0', 'link-96');">t0</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L833"></a><tt class="py-lineno">833</tt>  <tt class="py-line">            <tt class="py-name">wr</tt> <tt class="py-op">=</tt> <tt class="py-name">maxw</tt><tt class="py-op">/</tt><tt class="py-name">minw</tt> </tt>
<a name="L834"></a><tt class="py-lineno">834</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Likelihood ratio of best/worst retained runs: %s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">wr</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L835"></a><tt class="py-lineno">835</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">wr</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L836"></a><tt class="py-lineno">836</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Flat likelihood, trying again..."</tt> </tt>
<a name="L837"></a><tt class="py-lineno">837</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L838"></a><tt class="py-lineno">838</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Improvement: %s percent"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-number">100</tt><tt class="py-op">-</tt><tt class="py-number">100</tt><tt class="py-op">*</tt><tt class="py-name">wr</tt><tt class="py-op">/</tt><tt class="py-name">lr</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L839"></a><tt class="py-lineno">839</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L840"></a><tt class="py-lineno">840</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'Resampling weights are all zero, please check your model or data, and try again.\n'</tt> </tt>
<a name="L841"></a><tt class="py-lineno">841</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; Likelihood (min,mean,max): '</tt><tt class="py-op">,</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
<a name="L842"></a><tt class="py-lineno">842</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'==&gt; RMS deviation of outputs: %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="BIP.Bayes.Melding.Meld.basicfit" class="py-name" href="#" onclick="return doclink('link-130', 'basicfit', 'link-94');">basicfit</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L843"></a><tt class="py-lineno">843</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L844"></a><tt class="py-lineno">844</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L845"></a><tt class="py-lineno">845</tt>  <tt class="py-line"> </tt>
<a name="Meld.runModel"></a><div id="Meld.runModel-def"><a name="L846"></a><tt class="py-lineno">846</tt> <a class="py-toggle" href="#" id="Meld.runModel-toggle" onclick="return toggle('Meld.runModel');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding.Meld-class.html#runModel">runModel</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">savetemp</tt><tt class="py-op">,</tt><tt class="py-param">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">k</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meld.runModel-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Meld.runModel-expanded"><a name="L847"></a><tt class="py-lineno">847</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L848"></a><tt class="py-lineno">848</tt>  <tt class="py-line"><tt class="py-docstring">        Handles running the model k times keeping a temporary savefile for</tt> </tt>
<a name="L849"></a><tt class="py-lineno">849</tt>  <tt class="py-line"><tt class="py-docstring">        resuming calculation in case of interruption.</tt> </tt>
<a name="L850"></a><tt class="py-lineno">850</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L851"></a><tt class="py-lineno">851</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L852"></a><tt class="py-lineno">852</tt>  <tt class="py-line"><tt class="py-docstring">            - `savetemp`: Boolean. create a temp file?</tt> </tt>
<a name="L853"></a><tt class="py-lineno">853</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L854"></a><tt class="py-lineno">854</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> </tt>
<a name="L855"></a><tt class="py-lineno">855</tt>  <tt class="py-line">            <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">,</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L856"></a><tt class="py-lineno">856</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">k</tt><tt class="py-op">:</tt> </tt>
<a name="L857"></a><tt class="py-lineno">857</tt>  <tt class="py-line">            <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt> </tt>
<a name="L858"></a><tt class="py-lineno">858</tt>  <tt class="py-line"><tt class="py-comment">#       Running the model ==========================</tt> </tt>
<a name="L859"></a><tt class="py-lineno">859</tt>  <tt class="py-line">         </tt>
<a name="L860"></a><tt class="py-lineno">860</tt>  <tt class="py-line">                 </tt>
<a name="L861"></a><tt class="py-lineno">861</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L862"></a><tt class="py-lineno">862</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L863"></a><tt class="py-lineno">863</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L864"></a><tt class="py-lineno">864</tt>  <tt class="py-line">            <tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L865"></a><tt class="py-lineno">865</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L866"></a><tt class="py-lineno">866</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">cb</tt><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L867"></a><tt class="py-lineno">867</tt>  <tt class="py-line">            <tt class="py-docstring">'''</tt> </tt>
<a name="L868"></a><tt class="py-lineno">868</tt>  <tt class="py-line"><tt class="py-docstring">            callback function for the asynchronous model runs</tt> </tt>
<a name="L869"></a><tt class="py-lineno">869</tt>  <tt class="py-line"><tt class="py-docstring">            '''</tt> </tt>
<a name="L870"></a><tt class="py-lineno">870</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L871"></a><tt class="py-lineno">871</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt id="link-131" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-131', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-132" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-132', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L872"></a><tt class="py-lineno">872</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L873"></a><tt class="py-lineno">873</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt id="link-133" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-133', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt id="link-134" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-134', 'r', 'link-80');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">t</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-comment"># #phi is the last t points in the simulation</tt> </tt>
</div><a name="L874"></a><tt class="py-lineno">874</tt>  <tt class="py-line"> </tt>
<a name="L875"></a><tt class="py-lineno">875</tt>  <tt class="py-line">        <tt class="py-name">po</tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L876"></a><tt class="py-lineno">876</tt>  <tt class="py-line">        <tt id="link-135" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-135', 't0', 'link-96');">t0</a></tt><tt class="py-op">=</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L877"></a><tt class="py-lineno">877</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">k</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L878"></a><tt class="py-lineno">878</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q1theta</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt> </tt>
<a name="L879"></a><tt class="py-lineno">879</tt>  <tt class="py-line">            <tt id="link-136" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-136', 'r', 'link-80');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">po</tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="BIP.Bayes.Melding.enumRun" class="py-name" href="#" onclick="return doclink('link-137', 'enumRun', 'link-89');">enumRun</a></tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-138', 'model', 'link-17');">model</a></tt><tt class="py-op">,</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">callback</tt><tt class="py-op">=</tt><tt class="py-name">cb</tt><tt class="py-op">)</tt> </tt>
<a name="L880"></a><tt class="py-lineno">880</tt>  <tt class="py-line"><tt class="py-comment">#            r = po.apply_async(self.model,theta)</tt> </tt>
<a name="L881"></a><tt class="py-lineno">881</tt>  <tt class="py-line"><tt class="py-comment">#            if t == 1:</tt> </tt>
<a name="L882"></a><tt class="py-lineno">882</tt>  <tt class="py-line"><tt class="py-comment">#                phi[i] = (r.get()[-1],)</tt> </tt>
<a name="L883"></a><tt class="py-lineno">883</tt>  <tt class="py-line"><tt class="py-comment">#            else:</tt> </tt>
<a name="L884"></a><tt class="py-lineno">884</tt>  <tt class="py-line"><tt class="py-comment">#                phi[i] = [tuple(l) for l in r.get()[-t:]]# #phi is the last t points in the simulation</tt> </tt>
<a name="L885"></a><tt class="py-lineno">885</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L886"></a><tt class="py-lineno">886</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; K = %s"</tt><tt class="py-op">%</tt><tt class="py-name">i</tt> </tt>
<a name="L887"></a><tt class="py-lineno">887</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> </tt>
<a name="L888"></a><tt class="py-lineno">888</tt>  <tt class="py-line">                    <tt class="py-name">CP</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L889"></a><tt class="py-lineno">889</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">savetemp</tt><tt class="py-op">:</tt> <tt class="py-comment">#If all replicates are done, clear temporary save files.</tt> </tt>
<a name="L890"></a><tt class="py-lineno">890</tt>  <tt class="py-line">            <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">unlink</tt><tt class="py-op">(</tt><tt class="py-string">'phi.temp'</tt><tt class="py-op">)</tt> </tt>
<a name="L891"></a><tt class="py-lineno">891</tt>  <tt class="py-line">            <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">unlink</tt><tt class="py-op">(</tt><tt class="py-string">'q1theta'</tt><tt class="py-op">)</tt> </tt>
<a name="L892"></a><tt class="py-lineno">892</tt>  <tt class="py-line">        <tt class="py-name">po</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L893"></a><tt class="py-lineno">893</tt>  <tt class="py-line">        <tt class="py-name">po</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L894"></a><tt class="py-lineno">894</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"==&gt; Done Running the K (%s) replicates (took %s seconds)\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-139" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-139', 't0', 'link-96');">t0</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L895"></a><tt class="py-lineno">895</tt>  <tt class="py-line">         </tt>
<a name="L896"></a><tt class="py-lineno">896</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> </tt>
</div></div><a name="L897"></a><tt class="py-lineno">897</tt>  <tt class="py-line"> </tt>
<a name="L898"></a><tt class="py-lineno">898</tt>  <tt class="py-line"> </tt>
<a name="enumRun"></a><div id="enumRun-def"><a name="L899"></a><tt class="py-lineno">899</tt> <a class="py-toggle" href="#" id="enumRun-toggle" onclick="return toggle('enumRun');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding-module.html#enumRun">enumRun</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt><tt class="py-param">theta</tt><tt class="py-op">,</tt><tt class="py-param">k</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="enumRun-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="enumRun-expanded"><a name="L900"></a><tt class="py-lineno">900</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L901"></a><tt class="py-lineno">901</tt>  <tt class="py-line"><tt class="py-docstring">    Returns model results plus run number.</tt> </tt>
<a name="L902"></a><tt class="py-lineno">902</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L903"></a><tt class="py-lineno">903</tt>  <tt class="py-line"><tt class="py-docstring">    :Parameters:</tt> </tt>
<a name="L904"></a><tt class="py-lineno">904</tt>  <tt class="py-line"><tt class="py-docstring">        - `model`: model callable</tt> </tt>
<a name="L905"></a><tt class="py-lineno">905</tt>  <tt class="py-line"><tt class="py-docstring">        - `theta`: model input list</tt> </tt>
<a name="L906"></a><tt class="py-lineno">906</tt>  <tt class="py-line"><tt class="py-docstring">        - `k`: run number</tt> </tt>
<a name="L907"></a><tt class="py-lineno">907</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L908"></a><tt class="py-lineno">908</tt>  <tt class="py-line"><tt class="py-docstring">    :Return:</tt> </tt>
<a name="L909"></a><tt class="py-lineno">909</tt>  <tt class="py-line"><tt class="py-docstring">        - res: result list</tt> </tt>
<a name="L910"></a><tt class="py-lineno">910</tt>  <tt class="py-line"><tt class="py-docstring">        - `k`: run number</tt> </tt>
<a name="L911"></a><tt class="py-lineno">911</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L912"></a><tt class="py-lineno">912</tt>  <tt class="py-line">    <tt class="py-name">res</tt> <tt class="py-op">=</tt><tt id="link-140" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-140', 'model', 'link-17');">model</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L913"></a><tt class="py-lineno">913</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">,</tt><tt class="py-name">k</tt><tt class="py-op">)</tt> </tt>
</div><a name="L914"></a><tt class="py-lineno">914</tt>  <tt class="py-line"> </tt>
<a name="L915"></a><tt class="py-lineno">915</tt>  <tt class="py-line"> </tt>
<a name="L916"></a><tt class="py-lineno">916</tt>  <tt class="py-line"> </tt>
<a name="model"></a><div id="model-def"><a name="L917"></a><tt class="py-lineno">917</tt> <a class="py-toggle" href="#" id="model-toggle" onclick="return toggle('model');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding-module.html#model">model</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt> <tt class="py-param">p0</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="model-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="model-expanded"><a name="L918"></a><tt class="py-lineno">918</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L919"></a><tt class="py-lineno">919</tt>  <tt class="py-line"><tt class="py-docstring">    Model (r,p0, n=1)</tt> </tt>
<a name="L920"></a><tt class="py-lineno">920</tt>  <tt class="py-line"><tt class="py-docstring">    Simulates the Population dynamic Model (PDM) Pt = rP0</tt> </tt>
<a name="L921"></a><tt class="py-lineno">921</tt>  <tt class="py-line"><tt class="py-docstring">    for n time steps.</tt> </tt>
<a name="L922"></a><tt class="py-lineno">922</tt>  <tt class="py-line"><tt class="py-docstring">    P0 is the initial population size. </tt> </tt>
<a name="L923"></a><tt class="py-lineno">923</tt>  <tt class="py-line"><tt class="py-docstring">    Example model for testing purposes.</tt> </tt>
<a name="L924"></a><tt class="py-lineno">924</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L925"></a><tt class="py-lineno">925</tt>  <tt class="py-line"><tt class="py-comment">#    print "oi"</tt> </tt>
<a name="L926"></a><tt class="py-lineno">926</tt>  <tt class="py-line">    <tt class="py-name">Pt</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt> <tt class="py-comment"># initialize the output vector</tt> </tt>
<a name="L927"></a><tt class="py-lineno">927</tt>  <tt class="py-line">    <tt class="py-name">P</tt> <tt class="py-op">=</tt> <tt class="py-name">p0</tt> </tt>
<a name="L928"></a><tt class="py-lineno">928</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L929"></a><tt class="py-lineno">929</tt>  <tt class="py-line">        <tt class="py-name">Pt</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-141" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-141', 'r', 'link-80');">r</a></tt><tt class="py-op">*</tt><tt class="py-name">P</tt> </tt>
<a name="L930"></a><tt class="py-lineno">930</tt>  <tt class="py-line">        <tt class="py-name">P</tt> <tt class="py-op">=</tt> <tt class="py-name">Pt</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L931"></a><tt class="py-lineno">931</tt>  <tt class="py-line">     </tt>
<a name="L932"></a><tt class="py-lineno">932</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">Pt</tt> </tt>
</div><a name="L933"></a><tt class="py-lineno">933</tt>  <tt class="py-line"> </tt>
<a name="L934"></a><tt class="py-lineno">934</tt>  <tt class="py-line"> </tt>
<a name="plotRaHist"></a><div id="plotRaHist-def"><a name="L935"></a><tt class="py-lineno">935</tt> <a class="py-toggle" href="#" id="plotRaHist-toggle" onclick="return toggle('plotRaHist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding-module.html#plotRaHist">plotRaHist</a><tt class="py-op">(</tt><tt class="py-param">arr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plotRaHist-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plotRaHist-expanded"><a name="L936"></a><tt class="py-lineno">936</tt>  <tt class="py-line">    <tt class="py-docstring">'''</tt> </tt>
<a name="L937"></a><tt class="py-lineno">937</tt>  <tt class="py-line"><tt class="py-docstring">    Plots a record array</tt> </tt>
<a name="L938"></a><tt class="py-lineno">938</tt>  <tt class="py-line"><tt class="py-docstring">    as a panel of histograms</tt> </tt>
<a name="L939"></a><tt class="py-lineno">939</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="L940"></a><tt class="py-lineno">940</tt>  <tt class="py-line">    <tt class="py-name">nv</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">arr</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L941"></a><tt class="py-lineno">941</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ceil</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-comment">#figure size</tt> </tt>
<a name="L942"></a><tt class="py-lineno">942</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L943"></a><tt class="py-lineno">943</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">arr</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L944"></a><tt class="py-lineno">944</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">nv</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L945"></a><tt class="py-lineno">945</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">hist</tt><tt class="py-op">(</tt><tt class="py-name">arr</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">bins</tt><tt class="py-op">=</tt><tt class="py-number">50</tt><tt class="py-op">,</tt> <tt class="py-name">normed</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L946"></a><tt class="py-lineno">946</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L947"></a><tt class="py-lineno">947</tt>  <tt class="py-line"> </tt>
<a name="L948"></a><tt class="py-lineno">948</tt>  <tt class="py-line"> </tt>
<a name="main2"></a><div id="main2-def"><a name="L949"></a><tt class="py-lineno">949</tt> <a class="py-toggle" href="#" id="main2-toggle" onclick="return toggle('main2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding-module.html#main2">main2</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main2-expanded"><a name="L950"></a><tt class="py-lineno">950</tt>  <tt class="py-line">    <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L951"></a><tt class="py-lineno">951</tt>  <tt class="py-line">    <tt class="py-comment">#Me = Meld(K=5000,L=1000,model=model, ntheta=2,nphi=1,verbose=False,viz=False)</tt> </tt>
<a name="L952"></a><tt class="py-lineno">952</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="BIP.Bayes.Melding.Meld.setTheta" class="py-name" href="#" onclick="return doclink('link-142', 'setTheta', 'link-23');">setTheta</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'p0'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">,</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L953"></a><tt class="py-lineno">953</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="BIP.Bayes.Melding.Meld.setPhi" class="py-name" href="#" onclick="return doclink('link-143', 'setPhi', 'link-24');">setPhi</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'p'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt><tt class="py-number">9</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt><tt class="py-number">9</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L954"></a><tt class="py-lineno">954</tt>  <tt class="py-line">    <tt class="py-comment">#Me.add_data(normal(7.5,1,400),'normal',(6,9))</tt> </tt>
<a name="L955"></a><tt class="py-lineno">955</tt>  <tt class="py-line">    <tt class="py-comment">#Me.run()</tt> </tt>
<a name="L956"></a><tt class="py-lineno">956</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="BIP.Bayes.Melding.Meld.sir" class="py-name" href="#" onclick="return doclink('link-144', 'sir', 'link-26');">sir</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'p'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-number">7.5</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> <tt class="py-op">)</tt> </tt>
<a name="L957"></a><tt class="py-lineno">957</tt>  <tt class="py-line">    <tt id="link-145" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-145', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt> <tt class="py-op">=</tt> <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-146', 'getPosteriors', 'link-28');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L958"></a><tt class="py-lineno">958</tt>  <tt class="py-line">    <tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L959"></a><tt class="py-lineno">959</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">end</tt><tt class="py-op">-</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-string">' seconds'</tt> </tt>
<a name="L960"></a><tt class="py-lineno">960</tt>  <tt class="py-line">    <tt id="link-147" class="py-name" targets="Function BIP.Bayes.Melding.plotRaHist()=BIP.Bayes.Melding-module.html#plotRaHist"><a title="BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-147', 'plotRaHist', 'link-147');">plotRaHist</a></tt><tt class="py-op">(</tt><tt id="link-148" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-148', 'pt', 'link-27');">pt</a></tt><tt class="py-op">)</tt> </tt>
<a name="L961"></a><tt class="py-lineno">961</tt>  <tt class="py-line">    <tt id="link-149" class="py-name"><a title="BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-149', 'plotRaHist', 'link-147');">plotRaHist</a></tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt> </tt>
<a name="L962"></a><tt class="py-lineno">962</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L963"></a><tt class="py-lineno">963</tt>  <tt class="py-line">     </tt>
<a name="L964"></a><tt class="py-lineno">964</tt>  <tt class="py-line">     </tt>
<a name="mh_test"></a><div id="mh_test-def"><a name="L965"></a><tt class="py-lineno">965</tt> <a class="py-toggle" href="#" id="mh_test-toggle" onclick="return toggle('mh_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.Melding-module.html#mh_test">mh_test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="mh_test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="mh_test-expanded"><a name="L966"></a><tt class="py-lineno">966</tt>  <tt class="py-line">    <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L967"></a><tt class="py-lineno">967</tt>  <tt class="py-line">    <tt class="py-comment">#Me = Meld(K=5000,L=1000,model=model, ntheta=2,nphi=1,verbose=False,viz=False)</tt> </tt>
<a name="L968"></a><tt class="py-lineno">968</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="BIP.Bayes.Melding.Meld.setTheta" class="py-name" href="#" onclick="return doclink('link-150', 'setTheta', 'link-23');">setTheta</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'p0'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">,</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L969"></a><tt class="py-lineno">969</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="BIP.Bayes.Melding.Meld.setPhi" class="py-name" href="#" onclick="return doclink('link-151', 'setPhi', 'link-24');">setPhi</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'p'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt><tt class="py-number">9</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt><tt class="py-number">9</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L970"></a><tt class="py-lineno">970</tt>  <tt class="py-line">    <tt class="py-comment">#Me.add_data(normal(7.5,1,400),'normal',(6,9))</tt> </tt>
<a name="L971"></a><tt class="py-lineno">971</tt>  <tt class="py-line">    <tt class="py-comment">#Me.run()</tt> </tt>
<a name="L972"></a><tt class="py-lineno">972</tt>  <tt class="py-line">    <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="BIP.Bayes.Melding.Meld.mcmc_run" class="py-name" href="#" onclick="return doclink('link-152', 'mcmc_run', 'link-29');">mcmc_run</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'p'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-number">7.5</tt><tt class="py-op">]</tt><tt class="py-op">}</tt><tt class="py-op">,</tt><tt class="py-name">burnin</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt> </tt>
<a name="L973"></a><tt class="py-lineno">973</tt>  <tt class="py-line">    <tt id="link-153" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-153', 'pt', 'link-27');">pt</a></tt><tt class="py-op">,</tt><tt class="py-name">pp</tt> <tt class="py-op">=</tt> <tt class="py-name">Me</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="BIP.Bayes.Melding.Meld.getPosteriors" class="py-name" href="#" onclick="return doclink('link-154', 'getPosteriors', 'link-28');">getPosteriors</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L974"></a><tt class="py-lineno">974</tt>  <tt class="py-line">    <tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L975"></a><tt class="py-lineno">975</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">end</tt><tt class="py-op">-</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-string">' seconds'</tt> </tt>
<a name="L976"></a><tt class="py-lineno">976</tt>  <tt class="py-line">    <tt id="link-155" class="py-name"><a title="BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-155', 'plotRaHist', 'link-147');">plotRaHist</a></tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-156', 'pt', 'link-27');">pt</a></tt><tt class="py-op">)</tt> </tt>
<a name="L977"></a><tt class="py-lineno">977</tt>  <tt class="py-line">    <tt id="link-157" class="py-name"><a title="BIP.Bayes.Melding.plotRaHist" class="py-name" href="#" onclick="return doclink('link-157', 'plotRaHist', 'link-147');">plotRaHist</a></tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt> </tt>
<a name="L978"></a><tt class="py-lineno">978</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L979"></a><tt class="py-lineno">979</tt>  <tt class="py-line">     </tt>
<a name="L980"></a><tt class="py-lineno">980</tt>  <tt class="py-line"> </tt>
<a name="L981"></a><tt class="py-lineno">981</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L982"></a><tt class="py-lineno">982</tt>  <tt class="py-line">    <tt class="py-name">Me</tt> <tt class="py-op">=</tt> <tt id="link-158" class="py-name"><a title="BIP.Bayes.Melding.Meld" class="py-name" href="#" onclick="return doclink('link-158', 'Meld', 'link-16');">Meld</a></tt><tt class="py-op">(</tt><tt class="py-name">K</tt><tt class="py-op">=</tt><tt class="py-number">5000</tt><tt class="py-op">,</tt><tt class="py-name">L</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">,</tt><tt id="link-159" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-159', 'model', 'link-17');">model</a></tt><tt class="py-op">=</tt><tt id="link-160" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-160', 'model', 'link-17');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">ntheta</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nphi</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">verbose</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-name">viz</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L983"></a><tt class="py-lineno">983</tt>  <tt class="py-line">    <tt id="link-161" class="py-name" targets="Function BIP.Bayes.Melding.mh_test()=BIP.Bayes.Melding-module.html#mh_test"><a title="BIP.Bayes.Melding.mh_test" class="py-name" href="#" onclick="return doclink('link-161', 'mh_test', 'link-161');">mh_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L984"></a><tt class="py-lineno">984</tt>  <tt class="py-line">    <tt class="py-comment">#main2()</tt> </tt>
<a name="L985"></a><tt class="py-lineno">985</tt>  <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="BIP-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/bayesian-inference">Project Homepage</a></th>
          </tr></table></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Thu Jan  7 10:45:34 2010
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>
